In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential

Abstract

We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.

Characterization and Bioremediation potential of marine psychrotolerant Pseudomonas spp. isolated from the Mediterranean Sea, Egypt.

“…Numerous psychrophilic and psychrotolerant Pseudomonas strains have been isolated from Antarctica, (Reddy et al, 2004;Ma et al, 2006;Bozal et al, 2007, Orellana-Saez et al, 2019, Yarzabal et al, 2019, Divya et al, 2019.…”

“…Psychrotolerant bacteria grow well at temperatures near the freezing point of water, but the rate of growth increases at temperature above 20 °C (Margesin et al, 2007;Orellana-Saez et al, 2019). Bakermans et al (2006) reported that facultative psychrotolerant or cold adapted bacteria such as Psychrobacter cryohalolentis can grow in temperature ranges from 10 to 30 °C.…”

“…Cold adapted organisms, psychrophiles and psychrotrophs, inhabit both terrestrial and aquatic environments in polar and alpine regions, in the bulk of the ocean, in shallow subterranean regions, in the upper atmosphere, in refrigerated environments, and on plants and animals living in cold regions (Margesin et al, 2007). Psychrotolerant organisms grow well at temperatures close to the freezing point of water, but have the fastest growth rates above 20 ºC (Margesin et al, 2007;Orellana-Saez et al, 2019), whereas psychrophilic organisms grow faster at a temperature of 15 ºC or lower, but are unable to grow above 20ºC (Margesin et al, 2007).…”

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

“…It was considered that Pseudomonas sp. MPC6 can be exploited as a biopolymer factory (Orellana-Saez et al, 2019). In recent years, the combination of computational and structure-based analysis with evolutionary driven methods (including directed evolution or synthetic biology) has been significantly enhanced by identifying novel extreme enzymes with high industrial application potential (Acevedo-Rocha et al, 2013;Ibrahim et al, 2016).…”

Channelling carbon flux through the meta‐cleavage route for improved poly(3‐hydroxyalkanoate) production from benzoate and lignin‐based aromatics in Pseudomonas putida H

“…different bacteria, strains of P. putida are metabolically versatile (Poblete-Castro et al, 2019;Weimer et al, 2020) and most efficient in accumulating PHAs under nitrogen limitation (Prieto et al, 2016;Poblete-Castro et al, 2020). Previous studies have achieved high PHA production in pseudomonads mostly from sugars (Poblete-Castro, Rodriguez, et al, 2014;Borrero-de Acuña et al, 2014;Davis et al, 2015) and sugar alcohols such as glycerol Beckers et al, 2016;Pacheco et al, 2019;Orellana-Saez et al, 2019). However, microbes accumulate PHAs also on aromatic substrates (Widdel and Pfennig, 1981;Nikodinovic et al, 2008) and in line, PHA production was recently demonstrated from lignin-based compounds using P. putida KT2440 (Linger et al, 2014;Liu et al, 2017) and engineered mutant derivatives (Salvachúa et al, 2020).…”